User GuideΒΆ Introduction to FastSurfer System Requirements Expert usage FreeSurfer Downstream Modules Intended Use References Acknowledgements Quick Start Singularity or Docker Google Colab Installation Linux MacOS Windows Examples Example 1: FastSurfer Docker Example 2: FastSurfer Singularity Example 3: Native FastSurfer on subjectX with parallel processing of hemis Example 4: FastSurfer on multiple subjects Example 5: Quick Segmentation Example 6: Running FastSurfer on a SLURM cluster via Singularity FastSurfer Flags Required arguments Required for Docker when running surface module Segmentation pipeline arguments (optional) Surface pipeline arguments (optional) Some other flags (optional) Output files Segmentation module Cerebnet module HypVINN module Surface module Docker Support Pull FastSurfer from DockerHub FastSurfer Docker Image Creation Build docker image with attestation and provenance Singularity Support Singularity with the official FastSurfer Image Building your own FastSurfer Singularity Image FastSurfer Singularity Image Usage Singularity Best Practice Manual Edits What are Edits? What can be edited? Pipeline overview Possible Edits General process Bias field correction asegdkt_segfile Talairach registration White matter segmentation Pial surface placement Side effects of edits Guide for experienced FreeSurfer users What NOT to do Longitudinal Processing What is Longitudinal Processing How to Run Your Data Behind the Scenes: Final Statistics: References Security Policy Supported Versions Reporting a Vulnerability Contributor Covenant Code of Conduct Our Pledge Our Standards Our Responsibilities Scope Enforcement Attribution Contributing to FastSurfer Reporting Bugs Suggesting Enhancements Contributing Code Attribution FastSurfer License Apache License